| Event | Time | Date | Name | Meet | History |
|---|---|---|---|---|---|
| 50 Free | 18.47 | March 27, 2008 | Cesar Cielo Filho | NCAA Division I Mens Championships | |
| 100 Free | 40.92 | March 29, 2008 | Cesar Cielo Filho | NCAA Division I Mens Championships | |
| 200 Free | 1:31.18 | March 23, 2018 | Zach Apple | NCAA Division I Mens Championships | |
| 500 Free | 4:10.82 | March 28, 2024 | Mason Mathias | NCAA Division I Mens Championships | |
| 1000 Free | 8:51.45 | Jan. 20, 2023 | Mason Mathias | Auburn vs. Alabama | |
| 1650 Free | 14:37.59 | March 24, 2012 | Zane Grothe | NCAA Division I Mens Championships | |
| 50 Back | 20.92 | March 27, 2024 | Nate Stoffle | NCAA Division I Mens Championships | |
| 100 Back | 44.89 | Feb. 17, 2023 | Nate Stoffle | SEC Championships | |
| 200 Back | 1:38.36 | March 30, 2024 | Aidan Stoffle | NCAA Division I Mens Championships | |
| 50 Breast | 26.09 | Feb. 28, 2020 | Tyler Babinec | SE AUB Auburn Classic | |
| 100 Breast | 51.06 | March 24, 2023 | Reid Mikuta | NCAA Division I Mens Championships | |
| 200 Breast | 1:52.09 | Feb. 19, 2022 | Reid Mikuta | SEC Championships | |
| 50 Fly | 21.81 | Oct. 9, 2015 | Arthur Mendes | War Eagle Invitational | |
| 100 Fly | 44.63 | March 27, 2009 | Tyler McGill | NCAA Division I Mens Championships | |
| 200 Fly | 1:40.59 | Feb. 19, 2016 | Hugo Morris | Southeastern Conference Championships | |
| 100 IM | 50.62 | Jan. 4, 2020 | Brogan Davis | Auburn vs. Virginia | |
| 200 IM | 1:40.67 | Feb. 15, 2018 | Hugo Gonzalez | Southeastern Conference Championships | |
| 400 IM | 3:35.76 | Feb. 16, 2018 | Hugo Gonzalez | Southeastern Conference Championships | |
| 200 Free Relay | 1:14.08 | March 26, 2009 | Andkjaer, Louw, Targett | NCAA Division I Mens Championships | |
| 400 Free Relay | 2:46.03 | Feb. 21, 2009 | Southeastern Conference Championships - Day Four - Finals | ||
| 800 Free Relay | 6:11.03 | Feb. 20, 2024 | Bonson, Husband, Schmidt, Mathias | SEC Championships | |
| 200 Medley Relay | 1:22.36 | March 27, 2009 | Targett, Louw | NCAA Division I Mens Championships | |
| 400 Medley Relay | 3:01.39 | March 26, 2009 | Klein, McGill, Targett | NCAA Division I Mens Championships |
